When milling a not too complex part, I am thinking it would be natural to mill the top first, then flip it over and do the bottom and then be done. For this to work, the system needs to be touched off on the flipped part somewhere, but where? At this point, the unfinished stock is exposed and there is nowhere reachable on the finished side (which is now underneath) to touch off against. In my mind, the only way would be to drill a hole through the entire stock at a known location (could be outside of the actual part or center of a hole in it, for instance). When flipping, the center of this hole would be a good origin/touch off point. This would get X and Y straight. However, FreeCAD only supports vertices as origins, not the center of a hole. What is the intended process to get the bottom aligned with the top?